[gmx-users] problem with g_density -center

Christopher Neale chris.neale at mail.utoronto.ca
Fri Oct 19 16:55:14 CEST 2012

Dear Ali:

Please also keep in mind that 99% of the papers published with gromacs using NpT have shown density profiles
along Z that were computed simply by using (the incorrect) trjconv -center and (the incorrect for NpT) g_density. 
So while I think that it's always important to get things right, if you're new to gromacs and/or scripting then maybe 
you should just use trjconv and g_density straight out of the box -- you won't be the first or the last to do so and
if you are seeing results that are way different than what you find in the literature then there is some other 
problem. A good place to start is to get 100 ns of sampling and run standard g_density.


-- original message --

Dear Chris

I found your topic:

    chris.neale | 21 Aug 01:30   ,   problem with g_density -center

The following text is your email. Is it correct?

I pursue your steps but :

1- I don't understand first commands that related to directories and :

   empty.mdp ?  and  command : avg=($(cat coord.xvg|grep -v '[@|#]' |
awk '{x+=$2;y+=$3;z+=$4;n++}
                                                END{print -1*x/n,-1*y/n}'))

2- I encounter with a problem in now make a new .tpr file, my error:

Fatal error:
Invalid line in tmpgro.gro for atom 1:
    1LI      C1    1   0.8   1.9   0.7

my top file is the same first top file in my simulation,

3- You can help me by simpler commands?

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